This paper presents an evaluation of the effectiveness of the removal of ammonia nitrogen from the water with oversize content of iron and manganese. The study was conducted using a two-stage biofiltration process on chalcedony beds. Biofilters operated in series, with counter-gravity flow at the first stage and the second stage gravity biofiltration. The chalcedony bed working at first stage was pre-activated with 0,3% KMnO4 in order to increase the efficiency of manganese removal. The test system was supplied with model solution made on the basis of a tap water with the addition of iron(II) 1g Fe/m3, manganese(II) 1 g Mn/m3, and ammonium 1,15-3,6 g N/m3 The results obtained during the study confirm that the biological processes of water treatment using a two-stage biofiltration through the chalcedony bed are effective in the removal of ammonia nitrogen from groundwater. Despite the diversification of mechanisms to remove these pollutants, the results indicate that the removal of ammonia nitrogen and manganese from water are competitive processes. The presence of manganese affects on the process of nitrification and ammonia nitrogen removal efficiency, and nitrification process may interfere with the effectiveness of manganese removal from water during formation of nitrification deposits. It was found that the presence of both iron and manganese affects the efficiency of the removal of ammonium and formation time of biofilm. Chemical activation biofilter of first stage had an impact on the efficiency of removal of ammonium and manganese ions, and the analysis of content of these pollutants shows that up to 10 day the chemical oxidation processes were dominated in working bed. It is difficult, however, explain the fact that in the second step of biofiltration manganese was removed with high efficiency from the outset of experiment, despite the lack of chemical activation. Previous studies have shown little effectiveness in removing manganese on the type chalcedony. A single-stage of biofiltration used in study was insufficient to carry out the nitrification process and obtain potable water for human consumption. After the first stage biofiltration water did not satisfy the requirements in terms of nitrite, and manganese. The increase in contact time through the use of second-stage of biofiltration allowed to obtain water that meets all the requirements for drinking water. Time for nitrifying chalcedony biofilter to reach full capacity was 64 days. The balance of nitrogen compounds and oxygen consumption shows the complexity of biofiltration. The real oxygen consumption was significantly lower than suggested by stoichiometric calculations and amounted to about 2 mg O2/dm3 per each mg of nitrogen removed, which can suggest that the removal of ammonia nitrogen on researched bed can occur not only in the process of nitrification. The Anammox process as well as the assimilation may have the contribute in the removal of ammonia nitrogen in the biofiltration process